soslibPy: Python Wrappers for the SBML ODE Solver Library

** Update (7-28-09): soslibPy has been repackaged in a new installer (follow the link above) that makes it easier to run the examples. The readme and tutorial have not been updated accordingly so I’ll give you brief instructions here. Open up a command prompt (go to Start –> All Programs –> Accessories –> Command Prompt) and change the directory to your soslibPy installation directory. By default, setup_soslib.exe installs to ‘c:\Program Files\soslib\’. In the command prompt, go to this directory by typing ‘cd c:\Program Files\soslib’. Then, you may run a very basic example by typing ‘runSoslibExample’. This prints 10 integration steps for a very simple ODE model. You may run a couple of more exciting examples by typing ‘runSoslibPythonExample -s <example script> -i <sbml model>’ where <example script> is replaced by the name of the example script you want to run and <sbml model> is replaced by the name of an SBML file. The names of the two example Python scripts provided with the installation are soslibPyTest.py and SLPyObjectsTest.py. There are also SBML files (*.xml) in the folder ‘examplesSoslib/sbmlModels/’. Be sure to include the full relative path to both the Python script and the SBML file. For example:

The first example above (soslibPyTest.py) can run with any SBML file. Look in the ‘examplesSoslib/sbmlModels/’ folder for other SBML files. The second example, however, should be run with testModel.xml since this Python script references a parameter named ‘k1’. If, however, you provide another SBML model that happens to have a parameter named ‘k1’, the example should run okay.

Python wrappers are available for CC3D permitting scripting access to its core functionality. Additional layers of Python have been written to extend the basic capabilities of CC3D and to allow more sophisticated multicellular modeling simulations. Recently, I created a Python wrapper library for the essential functions of SOSLib (SBML ODE Solver Library – written in C) that allow SBML-defined models to be read and numerically solved. SOSLib makes use of libSBML (for reading SBML files) and SUNDIALS (particularly CVODES, the ODE solver library). The wrappers were generated using SWIG.

The Windows download for soslibPy (see the top of this post) provides a couple of sample Python scripts (soslibPyTest.py and SLPyObjectsTest.py) demonstrating the use of the soslibPy library. These can be run at the Python command line by typing “from soslibPyTest import *” or “from SLPyObjectsTest import *”. Be sure to download and install Python 2.5. There are also a couple of CC3D simulation scripts (SLPyIntegrator.py and SLPyIntegrElowitz2000.py) that demonstrate how soslibPy can be used with CC3D. Be sure to download and install CompuCell3D 3.3.1. For details on how to run these examples, see “soslibPy_README.txt” and “soslibPy_TUTORIAL.txt” from the soslibPy installation.

Hello Ryan!my name is Sotiris, a PhD student in Nottingham University, UK. I was in Indiana last summer where you talked at the CC3D/SBW tutorial about SBW and CC3D using an example with Notch signaling. Do you have an email that i could contact you?
Many thanks!
Sotiris